PubMed search, ChatGPT summary, and sending an email in R

1. Search the PubMed database Use the entrez_search function from the rentrez package to search the PubMed database

library(rentrez)

date_start <- gsub("-", "/", Sys.Date()-2)
date_end <- gsub("-", "/", Sys.Date()-1)
search_query <- paste0("(typhoid OR cholera) AND ", date_start,":", date_end, "[dp]") # the search query
search_results <- entrez_search(db="pubmed", term=search_query) # any other useful parameters?

2. Fetch the details of the article in xml format

# Retrieve the details of the data in xml format based on pubmed ids
article_details <- entrez_fetch(db="pubmed", id=search_results$ids, rettype="xml")

3. Parse the XML using the xml2 package

library(xml2)
# Parse the XML data
doc <- read_xml(article_details)
# Extract the titles and abstracts
titles <- xml_text(xml_find_all(doc, "//ArticleTitle"))
# abstracts <- xml_text(xml_find_all(doc, "//AbstractText"))
abstracts <- xml_text(xml_find_all(doc, "//Abstract"))
dois <- xml_text(xml_find_all(doc, ".//PubmedData/ArticleIdList/ArticleId[@IdType='doi']")) # to get the doi's

4. Call ChatGPT to summarize the abstract in 1-2 sentences This is a subscription-based service. You must have a ChatGPT API key and must have signed up for their paid service.

# gpt-4o
prompt_chatgpt <- function(prompt, api_key=NULL, model="gpt-4o", temperature=0.8){
  model <- grep(model, c("gpt-3.5-turbo", "gpt-4o"), value=TRUE)
  response <- httr::POST(
    url = "https://api.openai.com/v1/chat/completions", 
    httr::add_headers(Authorization = paste("Bearer", api_key)),
    httr::content_type_json(),
    encode = "json",
    body = list(
      model = model,
      temperature = temperature, # this is the degree of randomness of the model's output
      messages = list(list(
        role = "user", 
        content = prompt
     ))
   )
  )
  return(httr::content(response)$choices[[1]]$message$content)
}

5. Make R send you an email everyday Use simple HTML syntaxes (<p></p> or <b></b>) to compose an email message using blastula package

library(blastula)

create_summary <- function(titles, abstract_summary, ids, dois) {
  summary <- sapply(1:length(abstract_summary), function(i) paste0("<p>", " <b>", " <a href=https://pubmed.ncbi.nlm.nih.gov/", ids[i], "/> ", titles[i], "</a>", " </b> ", abstract_summary[i], " PMID=", ids[i], " DOI=", dois[i], "</p>"))
  return(summary)
}

email <- compose_email(
  title = "Test Email",
  body = md(create_summary(titles, abstract_summary, ids, dois)))

email %>%
  smtp_send( 
    from = "kimfinale@gmail.com",
    to = "jonghoon.kim@ivi.int",
    subject = "Daily summary of PubMed search",
    # credentials = creds_key(id = "gmail"),
    credentials = creds_file("gmail_cred")
  )

6. Save all as a single R script

date_start <- gsub("-", "/", Sys.Date()-2)
date_end <- gsub("-", "/", Sys.Date()-1)
search_query <- paste0("(typhoid OR cholera OR transmission OR modeling) AND ", date_start,":", date_end, "[dp]") 
 
chatgpt_api_key <- Sys.getenv("CHATGPT_API_KEY")

search_res <- rentrez::entrez_search(db="pubmed", term=search_query)
model <- "gpt-3.5"  
if (length(search_res$ids) > 0) { # one or more hits
  ids <- search_res$ids
  details <- rentrez::entrez_fetch(db="pubmed", id=ids, rettype="xml")
  doc <- xml2::read_xml(details)
  titles <- xml2::xml_text(xml2::xml_find_all(doc, "//ArticleTitle"))
  abstracts <- xml2::xml_text(xml2::xml_find_all(doc, "//Abstract"))
  dois <- xml2::xml_text(xml2::xml_find_all(doc, "//PubmedData/ArticleIdList/ArticleId[@IdType='doi']"))
  
  abstract_summary <- rep(NA, length(abstracts))

  if (length(abstracts) > 1) {
    for (i in 1:length(abstracts)) {
      prompt <- paste0("Your task is to generate a short summary of a scientific article based on its title and abstract. Summarize the text delimited by triple backticks into a single sentence. Please do not repeat the title. ``` Title: ", titles[i], ". Abstract: ", abstracts[i], "```")
      abstract_summary[i] <- 
        prompt_chatgpt(prompt=prompt, api_key=chatgpt_api_key, model=model)
    }
  }
  # create a summary for the email  
  summary <- sapply(1:length(abstract_summary), 
                    function(i) paste0("<p>", " <b>", " <a href=https://pubmed.ncbi.nlm.nih.gov/", ids[i], "/> ", titles[i], "</a>", " </b> ", abstract_summary[i], " PMID=", ids[i], ". DOI=", dois[i], ". </p>"))

  intro <- paste0("<p>Please enjoy the articles retrieved from PubMed based on your search query, ", search_query, ", published between ", date_start, ", and ", date_end, ". Each article is accompanied by a one-sentence summary provided by the ChatGPT, ", model, ". For feedback, please contact Jong-Hoon Kim at jonghoon.kim@ivi.int.</p>")
  
  summary <- c(intro, summary)
  email <- blastula::compose_email(
    title = "Weekly summary of PubMed search",
    body =  blastula::md(summary))
  
  blastula::smtp_send(email, 
    from = "kimfinale@gmail.com",
    to = "jonghoon.kim@ivi.int",
    subject = "Daily summary of PubMed search",
    credentials = blastula::creds_file("gmail_creds")
  )

} else {
  "No articles matched your query." 
}

7. Register the file using the Windows task scheduler

library(taskscheduleR)
# Schedule the script to run daily at a specific time
taskscheduler_create(
  taskname = "PubMed_ChatGPT_Summary",
  rscript = "~/myblog/pubmed_chatgpt.R",
  schedule = "WEEKLY", starttime = "22:00", startdate = "02/06/2024")